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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PCLO
piccolo presynaptic cytomatrix protein
Chromosome 7 Β· 7q21.11
NCBI Gene: 27445Ensembl: ENSG00000186472.21HGNC: HGNC:13406UniProt: Q9Y6V0
80PubMed Papers
21Diseases
0Drugs
73Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingextracellular exosomeGABA-ergic synapsecytoskeleton organizationpontocerebellar hypoplasia type 3major depressive disorderalcohol drinkingtype 1 diabetes mellitus
✦AI Summary

PCLO encodes piccolo, a scaffold protein of the presynaptic active zone (CAZ) that organizes the structural and functional architecture of synapses. Piccolo participates in forming Piccolo-Bassoon transport vesicles (PTVs) that deliver presynaptic components along axons, and at mature synapses regulates spatial organization of synaptic vesicle clusters and the readily releasable pool 1. Beyond structural roles, PCLO functions in presynaptic protein ubiquitination through SIAH1 interaction, presynaptic autophagy regulation, and synapse-to-nucleus signaling via CTBP1 association, linking synaptic activity to gene expression changes. PCLO variants are implicated in multiple psychiatric disorders: genome-wide association studies identified PCLO among synaptic structure genes contributing to post-traumatic stress disorder risk 2, and SNP rs2522833 showed significant association with depressive disorders in meta-analysis 3. Expression and genetic variation studies implicate PCLO in bipolar disorder, with intronic SNP rs13438494 significantly associated with disease 4. Recent whole-exome sequencing identified PCLO as a schizophrenia risk gene carrying damaging rare variants 5, with this association conserved across diverse ancestral populations 6. These findings establish PCLO as a synaptic organizer with pleiotropic contributions to psychiatric disease susceptibility, though effect sizes remain modest.

Sources cited
1
PCLO encodes presynaptic active zone scaffold protein Piccolo involved in synapse assembly and function
PMID: 12175852
2
PCLO identified among synaptic structure/function genes as genome-wide significant risk locus for PTSD
PMID: 38637617
3
PCLO SNP rs2522833 shows significant association with depressive disorders in population-based study and meta-analysis
PMID: 19942622
4
PCLO intronic SNP rs13438494 associated with bipolar disorder and differential gene expression in prefrontal cortex
PMID: 21185011
5
PCLO identified as schizophrenia risk gene with rare coding variants at FDR 5% significance threshold
PMID: 40753099
6
PCLO identified as shared schizophrenia and autism risk gene with rare protein-truncating variants conserved across diverse populations
PMID: 36914870
Disease Associationsβ“˜21
pontocerebellar hypoplasia type 3Open Targets
0.63Moderate
major depressive disorderOpen Targets
0.47Moderate
alcohol drinkingOpen Targets
0.44Moderate
type 1 diabetes mellitusOpen Targets
0.42Moderate
irritable bowel syndromeOpen Targets
0.40Weak
Nausea and vomitingOpen Targets
0.38Weak
insomniaOpen Targets
0.37Weak
post-traumatic stress disorderOpen Targets
0.35Weak
open-angle glaucomaOpen Targets
0.35Weak
attention deficit hyperactivity disorderOpen Targets
0.35Weak
schizophreniaOpen Targets
0.35Weak
COVID-19Open Targets
0.33Weak
ovarian dysfunctionOpen Targets
0.32Weak
glaucomaOpen Targets
0.31Weak
bipolar disorderOpen Targets
0.31Weak
autism spectrum disorderOpen Targets
0.30Weak
corneal ulcerOpen Targets
0.29Weak
anxiety disorderOpen Targets
0.28Weak
Abnormality of refractionOpen Targets
0.28Weak
thyroid diseaseOpen Targets
0.28Weak
Pontocerebellar hypoplasia 3UniProt
Pathogenic Variants73
NM_033026.6(PCLO):c.1839_1840delinsAA (p.Cys613_Gln614delinsTer)Pathogenic
PCLO-related disorder|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 613
NM_033026.6(PCLO):c.9097+2T>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2026
NM_033026.6(PCLO):c.299del (p.Pro100fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 100
NM_033026.6(PCLO):c.801_804del (p.Asp268fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 268
NM_033026.6(PCLO):c.2243del (p.Pro748fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 748
NM_033026.6(PCLO):c.5065dup (p.Thr1689fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1689
NM_033026.6(PCLO):c.4585C>T (p.Arg1529Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1529
NM_033026.6(PCLO):c.12503_12504del (p.Arg4168fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 4168
NM_033026.6(PCLO):c.4786G>T (p.Glu1596Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1596
NM_033026.6(PCLO):c.11395C>T (p.Arg3799Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 3799
NM_033026.6(PCLO):c.8649G>A (p.Trp2883Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 2883
NM_033026.6(PCLO):c.3802C>T (p.Gln1268Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1268
NM_033026.6(PCLO):c.3991C>T (p.Gln1331Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1331
NM_033026.6(PCLO):c.14027del (p.Lys4676fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 4676
NM_033026.6(PCLO):c.2680C>T (p.Gln894Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 894
NM_033026.6(PCLO):c.4376_4393del (p.Leu1459_Glu1465delinsTer)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1459
NM_033026.6(PCLO):c.4454_4455del (p.Gln1485fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 1485
NM_033026.6(PCLO):c.10264C>T (p.Gln3422Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 3422
NM_033026.6(PCLO):c.13658dup (p.Met4553fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 4553
NM_033026.6(PCLO):c.14055dup (p.Gly4686fs)Likely pathogenic
Pontocerebellar hypoplasia type 3
β˜…β˜†β˜†β˜†2024β†’ Residue 4686
View on ClinVar β†—
Related Genes
RAB3AProtein interaction93%CTBP2Protein interaction90%RIMS2Protein interaction87%RABAC1Protein interaction87%RAPGEF4Protein interaction87%BSNProtein interaction70%
Tissue Expression6 tissues
Brain
100%
Heart
16%
Ovary
4%
Bone Marrow
3%
Lung
1%
Liver
1%
Gene Interaction Network
Click a node to explore
PCLORAB3ACTBP2RIMS2RABAC1RAPGEF4BSN
PROTEIN STRUCTURE
Preparing viewer…
PDB1UJD Β· NMR
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.19Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.15 [0.12–0.19]
RankingsWhere PCLO stands among ~20K protein-coding genes
  • #5,950of 20,598
    Most Researched80
  • #1,012of 5,498
    Most Pathogenic Variants73 Β· top quartile
  • #399of 17,882
    Most Constrained (LOEUF)0.19 Β· top 5%
Genes detectedPCLO
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder.
PMID: 38637617
Nat Genet Β· 2024
1.00
2
The PCLO gene and depressive disorders: replication in a population-based study.
PMID: 19942622
Hum Mol Genet Β· 2010
0.90
3
Gene expression and genetic variation data implicate PCLO in bipolar disorder.
PMID: 21185011
Biol Psychiatry Β· 2011
0.80
4
Gene structure and genetic localization of the PCLO gene encoding the presynaptic active zone protein Piccolo.
PMID: 12175852
Int J Dev Neurosci Β· 2002
0.70
5
Characterization of
PMID: 35328053
Genes (Basel) Β· 2022
0.60